Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1522 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0220432571 sf0220426703 2 20432571 1.75E-08 2.34E-06
vg0431095866 sf0430910755 4 31095866 4.41E-08 1.21E-06
vg0911777445 sf0911776444 9 11777445 5.85E-08 NA
vg0427788963 sf0427603823 4 27788963 9.85E-08 NA
vg1126875179 sf1126403566 11 26875179 1.47E-06 NA
vg1003008433 sf1003007410 10 3008433 2.92E-06 1.99E-06
vg0727849191 sf0727848198 7 27849191 6.82E-06 NA